rs244656

chr5-134114136-T-Achr5-134114136-T-Cchr5-134114136-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047417635.1(TCF7):c.26T>A(p.Val9Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,076 control chromosomes in the GnomAD database, including 45,223 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.76 (45223 hom., cov: 32)
• Consequence: TCF7 XM_047417635.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

Genes affected

TCF7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCF7	XM_047417635.1	c.26T>A	p.Val9Asp	missense_variant	1/10
TCF7	XM_047417634.1	c.26T>A	p.Val9Asp	missense_variant	1/11
TCF7	XM_047417636.1	c.26T>A	p.Val9Asp	missense_variant	1/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115711 AN: 151958 Hom.: 45216 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.982

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.770

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.761 AC: 115760 AN: 152076 Hom.: 45223 Cov.: 32 AF XY: 0.756 AC XY: 56209 AN XY: 74328

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.853

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.786

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.769

Alfa AF: 0.805 Hom.: 6221

Bravo AF: 0.752

Asia WGS AF: 0.770 AC: 2678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
Cadd	Benign	1.5
Dann	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs244656; hg19: chr5-133449827;